1/*
2Redistribution and use in source and binary forms, with or without
3modification, are permitted provided that the following conditions are met:
4
5    * Redistributions of source code must retain the above copyright
6    notice, this list of conditions and the following disclaimer.
7
8    * Redistributions in binary form must reproduce the above copyright
9    notice, this list of conditions and the following disclaimer in the
10    documentation and/or other materials provided with the distribution.
11
12    * Neither the name of "The Computer Language Benchmarks Game" nor the
13    name of "The Computer Language Shootout Benchmarks" nor the names of
14    its contributors may be used to endorse or promote products derived
15    from this software without specific prior written permission.
16
17THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
18AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
19IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
20ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
21LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
22CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
23SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
24INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
25CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
26ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
27POSSIBILITY OF SUCH DAMAGE.
28*/
29
30/*
31** The Computer Language Shootout
32** http://shootout.alioth.debian.org/
33** contributed by Mike Pall
34**
35** regex-dna benchmark using PCRE
36**
37** compile with:
38**   gcc -O3 -fomit-frame-pointer -o regexdna regexdna.c -lpcre
39*/
40
41#define __USE_STRING_INLINES
42#include <stdio.h>
43#include <string.h>
44#include <stdlib.h>
45#include <pcre.h>
46
47typedef struct fbuf {
48  char *buf;
49  size_t size, len;
50} fbuf_t;
51
52static void fb_init(fbuf_t *b)
53{
54  b->buf = NULL;
55  b->len = b->size = 0;
56}
57
58static char *fb_need(fbuf_t *b, size_t need)
59{
60  need += b->len;
61  if (need > b->size) {
62    if (b->size == 0) b->size = need;
63    else while (need > b->size) b->size += b->size;
64    if (!(b->buf = realloc(b->buf, b->size))) exit(1);
65  }
66  return b->buf+b->len;
67}
68
69#define FB_MINREAD	(3<<16)
70
71/* Read all of a stdio stream into dst buffer. */
72static size_t fb_readall(fbuf_t *dst, FILE *fp)
73{
74  char *dp;
75  int n;
76  for (dp = fb_need(dst, FB_MINREAD);
77       (n = fread(dp, 1, dst->size-dst->len, fp)) > 0;
78       dp = fb_need(dst, FB_MINREAD)) dst->len += n;
79  if (ferror(fp)) exit(1);
80  return dst->len;
81}
82
83/* Substitute pattern p with replacement r, copying from src to dst buffer. */
84static size_t fb_subst(fbuf_t *dst, fbuf_t *src, const char *p, const char *r)
85{
86  pcre *re;
87  pcre_extra *re_ex;
88  const char *re_e;
89  char *dp;
90  int re_eo, m[3], pos, rlen, clen;
91  if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
92  re_ex = pcre_study(re, 0, &re_e);
93  for (dst->len = 0, rlen = strlen(r), pos = 0;
94       pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
95       pos = m[1]) {
96    clen = m[0]-pos;
97    dp = fb_need(dst, clen+rlen);
98    dst->len += clen+rlen;
99    memcpy(dp, src->buf+pos, clen);
100    memcpy(dp+clen, r, rlen);
101  }
102  clen = src->len-pos;
103  dp = fb_need(dst, clen);
104  dst->len += clen;
105  memcpy(dp, src->buf+pos, clen);
106  return dst->len;
107}
108
109/* Count all matches with pattern p in src buffer. */
110static int fb_countmatches(fbuf_t *src, const char *p)
111{
112  pcre *re;
113  pcre_extra *re_ex;
114  const char *re_e;
115  int re_eo, m[3], pos, count;
116  if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
117  re_ex = pcre_study(re, 0, &re_e);
118  for (count = 0, pos = 0;
119       pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
120       pos = m[1]) count++;
121  return count;
122}
123
124static const char *variants[] = {
125  "agggtaaa|tttaccct",         "[cgt]gggtaaa|tttaccc[acg]",
126  "a[act]ggtaaa|tttacc[agt]t", "ag[act]gtaaa|tttac[agt]ct",
127  "agg[act]taaa|ttta[agt]cct", "aggg[acg]aaa|ttt[cgt]ccct",
128  "agggt[cgt]aa|tt[acg]accct", "agggta[cgt]a|t[acg]taccct",
129  "agggtaa[cgt]|[acg]ttaccct", NULL
130};
131
132static const char *subst[] = {
133  "B", "(c|g|t)", "D", "(a|g|t)",   "H", "(a|c|t)", "K", "(g|t)",
134  "M", "(a|c)",   "N", "(a|c|g|t)", "R", "(a|g)",   "S", "(c|g)",
135  "V", "(a|c|g)", "W", "(a|t)",     "Y", "(c|t)",   NULL
136};
137
138int main(int argc, char **argv)
139{
140  fbuf_t seq[2];
141  const char **pp;
142  size_t ilen, clen, slen;
143  int flip;
144  fb_init(&seq[0]);
145  fb_init(&seq[1]);
146  ilen = fb_readall(&seq[0], stdin);
147  clen = fb_subst(&seq[1], &seq[0], ">.*|\n", "");
148  for (pp = variants; *pp; pp++)
149    printf("%s %d\n", *pp, fb_countmatches(&seq[1], *pp));
150  for (slen = 0, flip = 1, pp = subst; *pp; pp += 2, flip = 1-flip)
151    slen = fb_subst(&seq[1-flip], &seq[flip], *pp, pp[1]);
152  printf("\n%zu\n%zu\n%zu\n", ilen, clen, slen);
153  return 0;
154}
155